Impact of Modular Architecture on Activity of Glycoside Hydrolase Family 5 Subfamily 8 Mannanases
Abstract
:1. Introduction
2. Results
2.1. Bioinformatics Analysis
2.2. Enzymatic Activity of EsGH5_8 and XcGH5_8
Origin (GenBank Accession; No. in Phylogenetic Tree) | Modular Structure of Charac. Protein | CGM-lv U/mg; 1/s (Relative 1, %) | CGM-hv U/mg; 1/s (Relative 1, %) | KGM U/mg 1/s (Relative 1, %) | GG U/mg; 1/s (Relative 1, %) | INM U/mg; 1/s (Relative 1, %) | Ref. |
---|---|---|---|---|---|---|---|
Eubacterium siraeum (CBK96294; #1) | GH5_8 | 625 ± 28.8; 397 ± 18.3 (97) | 578 ± 13.0; 367 ± 8.3 (90) | 644 ± 11.4; 409 ± 7.2 (100) | 3.6 ± 0.2; 2.3 ± 0.1 (0.6) | 7.5 ± 0.1; 4.8 ± 0.1 (1.2) | Present study |
Saccharophagus degradans (ABD79918; #5) | GH5_8-CBM10x3 | 1972 ± 80; 1729 ± 70 (56) | 2212 ± 78; 1939 ± 68 (62) | 3544 ± 110; 3107 ± 96 (100) | 40 ± 8; 35 ± 7 (1.1) | 9 ± 1; 8 ± 1 (0.3) | [18] |
GH5_8-ΔCBM10x3 | 2906 ± 53; 1695 ± 31 (64) | 3151 ± 304; 1838 ± 177 (69) | 4556 ± 108; 2658 ± 63 (100) | 108 ± 25; 63 ± 15 (2.4) | 81 ± 7; 47 ± 4 (1.8) | [18] | |
Xanthomonas citri (AMU98328; #7) | GH5_8 | 713 ± 12.0; 414 ± 7.0 (100) | 709 ± 23.0; 411 ± 13,3 (99) | 247 ± 19.3; 143 ± 11.2 (35) | 1.1 ± 0.1; 0.6 ± 0.1 (0.2) | N.D. 2 | Present study |
Bifidobacterium animalis (ACS46797; #11) | GH5_8-CBM10 | 1380; 872 (55) | 1920; 1213 (76) | 2520; 1592 (100) | N.D. 2 | 120; 76 (5) | [19] |
Cellulosimicrobium sp. strain HY-13 (AEE43708; #12) | GH5_8-CBM10x2 | 8498 ± 105; 6232 ± 77 (58) | - | - | 967 ± 18; 709 ± 13 (6.6) | 14,711 ± 183; 10,788 ± 134 (100) | [21] |
Streptomyces sp. S27 (ADK91085; #14) | GH5_8-CBM10 | 2107 ± 182; 1510 ± 130 (100) | - | 1312 ± 110; 940 ± 79 (62) | 74 ± 12; 53 ± 8.6 (3.5) | - | [22] |
Streptomyces lividans (AAA26710; #15) | GH5_8-CBM10 | 141 ± 1.7 3,4 (100) | - | 55 ± 0.7 4 (39) | 21 ± 1.7 4 (15) | 18.8 ± 1.2 4 (13) | [23] |
GH5_8-ΔCBM10 | 97 ± 1.4 3,4 (100) | - | 61 ± 0.45 4 (63) | 23 ± 3.1 4 (23) | 19 ± 0.7 4 (20) | [23] | |
Streptomyces thermoluteus (BAM62868; #20) | GH5_8-CBM2 | 51 ± 1.6 3,4 (78) | - | 66 ± 1.5 4 (100) | 27 ± 1.4 4 (41) | 20.5 ± 0.4 4 (31) | [23] |
StGH5_8-ΔCBM2 | 39 ± 0.6 3,4 (86) | - | 45 ± 0.5 4 (100) | 20 ± 3.7 4 (44) | 14 ± 1.3 4 (32) | [23] |
Origin (Genbank Accession; No. in Phylogenetic Tree) | Modular Structure of Charac. Protein | KM (mg/mL) | kcat (1/s) | kcat/KM (mg/(mL s) | Binding CGM? | Ref. |
---|---|---|---|---|---|---|
Eubacterium siraeum (CBK96294; #1) | GH5_8 | 4.6 ± 0.5 | 850 ± 47 | 185 ± 23 | Yes, weakly | Present study |
Bacillus sp. JAMB-602 (BAD99527; #2) | GH5_8-CBM59 | 3.1 | 135 1 | ND 2 | [24] | |
Bacillus agaradhaerens (AAN27517; #3) | GH5_8-CBM59 | 1.8 | 633 | 250 | ND 2 | [13] |
Bacillus nealsonii PN-11 (AGU71466; #4) | GH5_8-CBM59 | 7.2 ± 0.3 | 750 ± 55 3 | 104 ± 2 3 | ND 2 | [25] |
Saccharophagus degradans (ABD79918; #5) | GH5_8-CBM10x3 | 2.1 ± 0.1 | 2333 ± 55 | 1096 ± 71 | Yes, Kd < 0.125 mg/mL | [18] |
SdGH5_8-ΔCBM10x3 | 2.4 ± 0.1 | 3440 ± 75 | 1413 ± 82 | No | [18] | |
Cellvibrio japonicus (ACE84673/AAO31759; #6) | GH5_8-ΔCBM10x2 | 8.5 ± 1.5 | 2381 ± 66 | 246.0 | No | [26] |
Xanthomonas citri (AMU98328; #7) | GH5_8 | 2.6 ± 0.3 | 732 ± 36 | 282 ± 35 | ND 2 | Present study |
Cellvibrio japonicus (AAO31760; #8) | GH5_8-ΔCBM10-CBM2 | 2.2 ± 0.3 | 1075 ± 27 | 446 | No | [26] |
Streptomyces thermolilacinus (BAK26781; #9) | GH5_8-ΔCBM2 | 4.9 ± 1.0 | 21 ± 2 | 4 ± 1 | ND 2 | [15,27] |
Streptomyces sp. SirexAA-E (AEN10237; #10) | GH5_8-Fn3-CBM2 | 2 ± 0.2 | 41 ± 2 | 21 ± 10 | Yes, weakly | [14] |
GH5_8-ΔFn3-CBM2 | 2 ± 0.4 | 41 ± 3 | 21 ± 8 | No | [14] | |
Bifidobacterium animalis (ACS46797; #11) | GH5_8-CBM10 | 1.6 ± 0.2 | 1828 ± 87 | 1157 ± 177 | Yes, Kd = 0.31 mg/ml | [19] |
GH5_8-ΔCBM10 | 1.8 ± 0.5 | 2005 ± 179 | 1146 ± 324 | No | [19] | |
Caldicellulosiruptor bescii (ACM60953; #13) | GH9-CBM3x3-GH5_8 | 0.6 ± 0.3 | 1420 ± 158 | 2290 | ND 2 | [28] |
CBM3x3-GH5_8 | 1.8 ± 0.5 | 3446 ± 367 | 1893 | ND 2 | [28] | |
Streptomyces sp. S27 (ADK91085; #14) | GH5_8-CBM10 | 0.16 | 3739 3 | 23369 3 | ND 2 | [22] |
Streptomyces lividans (AAA26710; #15) | GH5_8-CBM10 | 3.5 ± 0.5 | 197 ± 11 | 60 ± 7 | ND 2 | [23] |
GH5_8-ΔCBM10 | 4.3 ± 0.7 | 139 ± 9 | 33 ± 4 | ND 2 | [23] | |
Thermobifida halotolerans (AHB89704; #16) | GH5_8-CBM2 | 1.3 ± 0.3 | 78 ± 9 | 60 | ND 2 | [29] |
Thermobifida cellulosilytica (AHB89703; #17) | GH5_8-CBM2 | 0.8 ± 0.2 | 89 ± 5 | 106 | ND 2 | [29] |
Thermobifida fusca (AAZ54938; #18) | GH5_8-ΔCBM2 | 10.4 ± 2.6 | 96 ± 14 | 9 ± 3 | ND 2 | [15] |
Thermobifida fusca TM51 (AHB89702; #19) | GH5_8-CBM2 | 1.7 ± 0.4 | 122 ± 11 | 74 | ND 2 | [29] |
Streptomyces thermoluteus (BAM62868; #20) | GH5_8-CBM2 | 5.5 ± 1.6 | 101 ± 17 | 18 ± 3 | ND 2 | [23] |
GH5_8-ΔCBM2 | 5.5 ± 1.5 | 75 ± 12 | 14 ± 2 | ND 2 | [23] |
2.3. Polysaccharide Interaction
3. Discussion
4. Materials and Methods
4.1. Carbohydrates
4.2. Bioinformatics Analysis of GH5_8
4.3. Recombinant Protein Production
4.4. Protein Purification
4.5. Determination of Melting Temperature
4.6. Enzymatic Assays
4.7. Thin Layer Chromatography (TLC)
4.8. Affinity Gel-Electrophoresis (AGE)
4.9. Pull-Down Assay
Supplementary Materials
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Sample Availability
References
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Møller, M.S. Impact of Modular Architecture on Activity of Glycoside Hydrolase Family 5 Subfamily 8 Mannanases. Molecules 2022, 27, 1915. https://doi.org/10.3390/molecules27061915
Møller MS. Impact of Modular Architecture on Activity of Glycoside Hydrolase Family 5 Subfamily 8 Mannanases. Molecules. 2022; 27(6):1915. https://doi.org/10.3390/molecules27061915
Chicago/Turabian StyleMøller, Marie Sofie. 2022. "Impact of Modular Architecture on Activity of Glycoside Hydrolase Family 5 Subfamily 8 Mannanases" Molecules 27, no. 6: 1915. https://doi.org/10.3390/molecules27061915